Build GTB for MAF

The Mutation Annotation Format (MAF)) is a tab-delimited text file format that consolidates somatic mutation annotation results for all samples, allowing the SNVs and corresponding annotation information for all samples to be contained in a single file. The same mutation information is organized in the form of (chromosome, coordinate, optional alleles). On the command line, use the following command to build GTB archives for MAF files:

java -jar gbc.jar maf2gtb <input> [output] [options]

[!NOTE|label:Example|style:callout]

Use GBC to build an archive for the example file https://pmglab.top/gbc/download/all_QC_mutation_profile.maf and liftover the version of the reference genome from hg19 to hg38:

# Download the data file
wget https://pmglab.top/gbc/download/all_QC_mutation_profile.maf -O all_QC_mutation_profile.maf

# Run directly in the terminal
java -jar gbc.jar maf2gtb ./all_QC_mutation_profile.maf ./all_QC_mutation_profile.hg38.gtb \
                          --liftover hg19ToHg38

# Run it using docker
docker run -v `pwd`:`pwd` -w `pwd` --rm -it -m 4g gbc \
maf2gtb ./all_QC_mutation_profile.maf ./all_QC_mutation_profile.hg38.gtb \
        --liftover hg19ToHg38

Program Options

Usage: maf2gtb <input> [output] [options]
Java-API: edu.sysu.pmglab.gbc.MAF2GTB
About: Compress and build *.gtb (genotype block format) for *.maf (mutation 
       annotation format).
Options:
  --chromosome  Specify the chromosome tags file. e.g., identify 'X, chrX, 
                CHRX, ChrX' as '(int) 22' chromosome.
                format: --chromosome <file>
  --threads,-t  Set the number of threads.
                default: 4
                format: --threads <int>
  --add-meta    Add the specified metas to the output file.
                format: --add-meta <key>=<value> <key>=<value> ...
  --field       Set the field that records the cumulative number of mutations.
                default: Tumor_Allele_Count
                format: --field <string>
  --liftover    Lift over variants from one reference genome version to another 
                (chain files are downloaded from 
                http://hgdownload.cse.ucsc.edu/goldenPath/<version>/liftOver). 
                format: --liftover <string> 
                ([hg19ToHg38/hg38ToHg19/hg18ToHg19/hg18ToHg38] (ignoreCase))

API Toolkit

The API tool for converting MAF files to GTB files is edu.sysu.pmglab.gbc.MAF2GTB and is used in the following example:

MAF2GTB.of("https://pmglab.top/gbc/download/all_QC_mutation_profile.maf")
        .setOutputFile(new File("./all_QC_mutation_profile.hg38.maf"))
        .liftOver(RefGenomeVersion.hg19, RefGenomeVersion.hg38)
        .convert();